[emboss-dev] [BioLib-dev] R: EMBOSS 6.3.0 released - SAM/BAM

Peter biopython at maubp.freeserve.co.uk
Fri Jul 16 11:08:11 UTC 2010

On Fri, Jul 16, 2010 at 11:42 AM, Raoul Bonnal <bonnalraoul at ingm.it> wrote:
> Probably considering our idea of interoperability it would be reasonable to
> focus on the emboss implementation.
> We can check the performances of the Emboss and then converge on it and
> help in development if needed.

I haven't looked at the EMBOSS code, but I assume it is currently geared towards
looking at the reads as individual sequences - much like FASTQ and
most other file
formats supported by EMBOSS (and much like my own experiments for Biopython).
This makes perfect sense for extending the existing EMBOSS tools to work with
SAM/BAM. Is this a fair description Peter R?

On the other hand, the samtools C API is very rich and allows a lot of alignment
based operations (e.g. access to reads based on mapped position to a reference).
Isn't the samtools C API a broader more useful code base to wrap in the Bio*
projects? It will also be kept up to date with the expected file format changes.

Perhaps Pjotr could clarify what he has in mind for BioLib?


Peter C.

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